[buster-discuss] Beryllium ion refinement
ClaytonG at NJHealth.org
Fri Aug 31 20:34:42 CEST 2012
Great than you Oliver!
I will give it a try.
On Aug 31, 2012, at 12:08 PM, Oliver Smart wrote:
> On Fri, 31 Aug 2012, Clayton, Gina wrote:
>>> I have an unusual ion in my structure - a Be2+ ion (at least 1). It is
>>> surrounded by acidic residues which should be tetrahedral in
>>> arrangement and are more or less in that position without the ion
>>> modeled. I am wondering how I can best refine this ion in BUSTER.
>>> Be2+ forms partially covalent complexes with short distances, for
>>> example BeFl4 distance to each Fl is aprox 1.5Ang. I am guessing I have
>>> something of this nature in the structure but restrained by the side
>>> chains themselves i.e. not free oxides. I have the Be ion defined as
>>> given by my buster log file - which told me how to define the ion.
>>> However refinement moves the Be ion out of the +ve density peak into a
>>> zero density area.
>>> Do you have any ideas how I can specify this ion and at all?
> Please find attached a pdf that shows how a Be2+ ion with contacts to
> acidic residues should be handled. There is a corrected contact.dat
> and an example Gelly file.
> If anything is unclear please let us know.
> | Dr Oliver Smart |
> | Global Phasing Ltd., Cambridge UK |
> | http://www.globalphasing.com/people/osmart/ |
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